\HeaderA{compareComplex}{A function to compare two bipartite graph matrices}{compareComplex}
\keyword{array}{compareComplex}
\keyword{datagen}{compareComplex}
\begin{Description}\relax
The \code{\LinkA{compareComplex}{compareComplex}} function takes two bipartite graph matrix
representations and calculates three statistics between all pairs of
complexes, C-i and K-j: (1) the intersection between C-i and K-j, (2) the
proteins in C-i and not in K-j, (3) the proteins in K-j and not in
C-i. These stats are later used to calculate Jaccard and Dice-Sorenson
Coefficients as well as probability distributions of a protein p in a
complex C.
\end{Description}
\begin{Usage}
\begin{verbatim}
compareComplex(BGMat1, BGMat2)
\end{verbatim}
\end{Usage}
\begin{Arguments}
\begin{ldescription}
\item[\code{BGMat1}] The first bipartite graph matrix
\item[\code{BGMat2}] The second bipartite graph matrix
\end{ldescription}
\end{Arguments}
\begin{Details}\relax
The main point to remember is that we don't compare complexes within
the same matrix. We only compare pairs of complexes from the BGMat1 and
BGMat2. The \code{\LinkA{runCompareComplex}{runCompareComplex}} function must be
called first since all the labelled vertices present in BGMat1
must be present in the BGMat2 and vice versa so a true comparison can
be made.
\end{Details}
\begin{Value}
A list with the following entries:

\begin{ldescription}
\item[\code{intersect}] A matrix of pairwise intersections of the complexes
of BGMat1 and BGMat2
\item[\code{cminusk}] A matrix of the setdiff of the complexes of BGMat1 and
those of BGMat2
\item[\code{kminusc}] A matric of the setdiff of the complexes of BGMat2 and
those of BGMat1
\end{ldescription}
\end{Value}
\begin{Author}\relax
Tony Chiang
\end{Author}

